We reconstructed a phylogenetic tree of Chinese vascular plants (Trac
heophyta) using sequences of t
he chloroplast genes
atpB,
matK,
ndhF, and
rbcL and mitochondrial
matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. T
he compre
hensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. T
he infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of
Eberhardtia are sister to a clade formed by all ot
her taxa of Sapotaceae, except
Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for t
he creation of subtrees via SoTree (
http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.